Version 0.7.2
A variety of mostly minor improvements and bug fixes over v0.7.1.
segment, gainloss, segmetrics:
- Don't exclude very-low-coverage bins from calculations by default;
instead, expose this option as `--drop-low-coverage`. (This option
usually helps on tumor samples with some normal contamination, but leads
to problems on germline samples with homozygous deletions.)
segment:
- Output .cns files now have a "weight" column which is the mean of the
weights of the bins it covers.
- Output of the 'haar' segmentation method now has each segment's gene
names listed, as with the other methods.
- Fixed a bug where every segment's probe count (the "probes" column) could
be overwritten with the `_` character. (#53; thanks @chapmanb)
segmetrics:
- Each statistic is now printed in its own column, instead of squeezing all
stats into the "gene" column. The confidence/prediction interval stats
get two columns, `_lo` and `_hi` (lower and upper bound).
loh, scatter:
- Given a VCF called on a tumor-normal pair, use the paired normal to
select appropriate germline SNPs for plotting.
export:
- New format "nexus-ogt" combines bin-level copy number ratios with
b-allele frequencies given a VCF and a .cnr file. This replaces
"nexus-basic" with the `-v` option that was introduced in v0.7.1;
"nexus-ogt" stores the same info but can be viewed in BioDiscovery Nexus
Copy Number without any special configuration (load it as the
"Custom-OGT" data format).
- Renamed `bed` option `--show-neutral` to `--show-all`.
- `vcf` option `-g`/`--gender` now works properly for identifying CNVs on
sex chromosomes.
call:
- Fixed the `threshold` method to calculate absolute copy number on sex
chromosomes correctly (#49; thanks @tskir).